R Notebook
This is an R Markdown Notebook. When you execute code within the notebook, the results appear beneath the code.
Try executing this chunk by clicking the Run button within the chunk or by placing your cursor inside it and pressing Cmd+Shift+Enter.
library("devtools")
install_github("jw156605/SLICER")Skipping install of 'SLICER' from a github remote, the SHA1 (cb1be8ac) has not changed since last install.
Use `force = TRUE` to force installationlibrary(Seurat)
library(readr)
library(tidyverse)
library(HGC)
library(latticeExtra)
library(lattice)
library(RColorBrewer)
library(clusterProfiler)
library(org.Mm.eg.db)
library(AnnotationDbi)exp = read_csv("normalized_data.csv")New names:
• `` -> `...1`
• `` -> `...151`
• `` -> `...240`
• `` -> `...289`
• `` -> `...352`
• `` -> `...391`
• `` -> `...394`
• `` -> `...450`
• `` -> `...462`
Rows: 14414 Columns: 463
── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): ...1
dbl (454): M1_A01, M1_A02, M1_A03, M1_A05, M1_A06, M1_A08, M1_A09, M1_A10, M1_B01, M1_B03, M1_B04, M1_B05, M1_B06, M...
lgl (8): ...151, ...240, ...289, ...352, ...391, ...394, ...450, ...462
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.exp = discard(exp,~all(is.na(.) |. == ""))
exp = distinct(exp, `...1`, .keep_all = TRUE)
# filtering out the reprogramming transcription factors
exp = filter(exp, !`...1`%in% c("Mef2c", "Gata4", "Tbx5"))
exp = column_to_rownames(exp, var="...1")
seurat.obj = CreateSeuratObject(counts = exp)seurat.obj = NormalizeData(seurat.obj)Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|seurat.obj = FindVariableFeatures(seurat.obj, selection.method = "vst", nfeatures = 10000)Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|all.genes = rownames(seurat.obj)
seurat.obj = ScaleData(seurat.obj, features = all.genes)Centering and scaling data matrix
|
| | 0%
|
|======= | 7%
|
|=============== | 13%
|
|====================== | 20%
|
|============================= | 27%
|
|===================================== | 33%
|
|============================================ | 40%
|
|=================================================== | 47%
|
|=========================================================== | 53%
|
|================================================================== | 60%
|
|========================================================================= | 67%
|
|================================================================================= | 73%
|
|======================================================================================== | 80%
|
|=============================================================================================== | 87%
|
|======================================================================================================= | 93%
|
|==============================================================================================================| 100%seurat.obj = RunPCA(seurat.obj, features = VariableFeatures(seurat.obj))PC_ 1
Positive: Ehd4, Acaa2, Dsp, Ldhb, Nid2, Ryr2, Myl4, Epb4.1, Smpx, Tnni3
Ttn, Tnnt2, Mgst3, Sort1, Ldb3, Jup, Mlf1, Baiap2l1, Rrad, Mgrn1
Fryl, Ppp1r3c, Fam134b, Fabp3, Cenpa, Usp28, Clu, Pcyt1a, Ddit4l, Cd24a
Negative: Fstl1, Bgn, Cd200, Col3a1, Rbp1, Tagln2, Fam198b, Postn, Col1a2, Tagln
Fbln2, Rbms3, Lox, Fbn1, Loxl1, Dhrs3, Marcks, Col8a1, 11-Sep, Col5a2
Clca1, Lrrc8a, Spry2, Anxa1, Ogn, Nars, Gstm2, Fbln5, Asns, Acta2
PC_ 2
Positive: Top2a, Prc1, Smc2, Ccnb1, Birc5, Cdk1, Ube2c, Rrm2, Mki67, Pbk
Ckap2l, Asf1b, Cks2, Tpx2, Cdca8, Kif20b, 2810417H13Rik, Cks1b, Anln, Tacc3
Spc25, Hmmr, Hmgb2, Shcbp1, Ndc80, Mad2l1, Nuf2, Cenpe, Ect2, Cdca2
Negative: Cst3, B2m, Sptbn1, Malat1, Ypel5, Itm2b, Gyg, Parp3, Tspyl1, Serpine2
Lama2, Igfbp7, Ogn, B4galt1, Gpx3, Ctsa, Asah1, Pdcd4, Itgb5, Fhl2
Pam, Col4a2, Lhfp, Tcn2, Mxra8, Smim14, Ctsd, Akap13, Prex2, Impact
PC_ 3
Positive: Cst3, Col4a1, Flna, Igfbp7, Col1a1, Col4a2, Myl9, Sorbs2, Fhl2, Itgb1
Tns1, Col14a1, Ankrd1, Tpm2, Lbh, Pcolce, Tuba1a, Postn, Tuba1b, Itga1
Col5a1, Actn4, Pdlim2, Myom1, Pdgfrb, Tbx20, Sorbs1, Acta2, Pcdh18, Macf1
Negative: Gpm6a, Mgst1, Hpgd, Gsta4, Ptgs1, Upk1b, Pkhd1l1, F11r, Msln, Bst1
Maf, Ezr, Mpzl2, Cxadr, Krt8, Cd55, Igfbp6, Igfbp4, Acsl4, Bex4
Gcnt1, Vnn1, Ftl1, Efna5, Slpi, Ptp4a2, Tmem108, Tmem154, Csde1, Bnc1
PC_ 4
Positive: S100a6, Tpm1, Tpm4, Actb, Nme1, Zyx, Lgals1, Tpm2, Cryab, Actg1
Wisp1, Gapdh, Gm12070, Actn1, Timp1, Slc25a5, Sec13, Eif5a, Psat1, Creb3l1
Tnfrsf12a, Ccnd2, Csf1, Pkm, Pcolce, Acta2, Des, Rcn3, Col1a1, Wdr1
Negative: Egfl7, Ctla2a, Gja4, Emcn, Cdh5, Notch1, Klhl4, Gimap6, Pecam1, Stab1
Gpr116, Lyl1, Tie1, Entpd1, Ctla2b, Fli1, Myct1, Sox7, Thsd1, Eltd1
Gngt2, Mmrn2, S1pr1, Mecom, Tgfbi, Klhl24, Tmem2, Apoe, Plxnd1, Akap13
PC_ 5
Positive: Egfl7, Notch1, Klhl4, Stab1, Cdh5, Emcn, Cgnl1, Pecam1, Gja4, Ramp2
Lyl1, Col4a1, Gpr116, Tie1, Entpd1, Zfp69, Loxl2, Eltd1, Plxnd1, Thsd1
Cxcl16, Col5a1, Tek, S1pr1, Txndc5, Tgfbi, Odc1, Eng, Sox7, Myct1
Negative: Spcs3, Impact, Ypel5, Cpne8, Lnp, Arhgap44, Sptbn1, Myo10, Nexn, Arid5b
Arl5a, Braf, Klhl9, Cpne3, Lama2, Mrfap1, Serping1, Mlf1, Zdhhc2, Mier3
Gm2a, Dstn, Emc2, Myoz2, Ncam1, Rhobtb3, Cryab, Gucy1a3, Ttn, Idh1 ElbowPlot(seurat.obj)seurat.obj = FindNeighbors(seurat.obj, dims = 1:15)Computing nearest neighbor graph
Computing SNNseurat.obj = FindClusters(seurat.obj, resolution = 1.75)Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 454
Number of edges: 16805
Running Louvain algorithm...0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|Maximum modularity in 10 random starts: 0.4797
Number of communities: 8
Elapsed time: 0 secondsidentified_cells = read.csv("paper_cell_states.csv", row.names = 1, header=TRUE)identified_cells = identified_cells[match(rownames(seurat.obj@meta.data), rownames(identified_cells)),]
seurat.obj@meta.data$cc_paper = identified_cells$CC
seurat.obj@meta.data$cat_paper = identified_cells$stage
seurat.obj@meta.data$cc_hclust = "CCI"
seurat.obj@meta.data[active_cells,]$cc_hclust = "CCA"
Idents(seurat.obj) = "RNA_snn_res.1.75"seurat.obj = RunUMAP(seurat.obj, dims = 1:15)Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session
17:59:25 UMAP embedding parameters a = 0.9922 b = 1.112
17:59:25 Read 454 rows and found 15 numeric columns
17:59:25 Using Annoy for neighbor search, n_neighbors = 30
17:59:25 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
17:59:25 Writing NN index file to temp file /var/folders/fj/09brpj8s5mz1c5wxktl80s080000gn/T//RtmpE0XJwn/file8ed51e4226b8
17:59:25 Searching Annoy index using 1 thread, search_k = 3000
17:59:25 Annoy recall = 100%
17:59:26 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
17:59:27 Initializing from normalized Laplacian + noise (using irlba)
17:59:27 Commencing optimization for 500 epochs, with 17028 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
17:59:28 Optimization finishedclusters = DimPlot(seurat.obj, group.by = "RNA_snn_res.1.75", label = TRUE, reduction = "umap")condition = DimPlot(seurat.obj, group.by = "cc_paper", label = TRUE, reduction = "umap")
condition|clusters
seurat.obj = RunTSNE(seurat.obj, dims = 1:15)
DimPlot(seurat.obj, reduction = "tsne", group.by = 'RNA_snn_res.1.75')
markers = FindAllMarkers(seurat.obj, logfc.threshold = 0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')top_markers = markers %>%
group_by(cluster) %>%
slice_max(n = 2, order_by = avg_log2FC)FeaturePlot(seurat.obj, features = c("Dhrs3"), min.cutoff = 'q10')
VlnPlot(seurat.obj, features = c("Rbp1", "Dhrs3"))
VlnPlot(seurat.obj, features = c("Fstl1", "Bgn"))
VlnPlot(seurat.obj, features = c("Serpinh1", "Dsp"))
VlnPlot(seurat.obj, features = c("Prc1", "Birc5"))
## cell cycle
s.genes <- str_to_title(cc.genes$s.genes)
g2m.genes <- str_to_title(cc.genes$g2m.genes)
seurat.obj = CellCycleScoring(seurat.obj, s.features = s.genes, g2m.features = g2m.genes)clusters = DimPlot(seurat.obj, group.by = "RNA_snn_res.1.75", label = TRUE, reduction = "umap")real_condition = DimPlot(seurat.obj, group.by = "cc_paper", label = TRUE, reduction = "umap") phase = DimPlot(seurat.obj, group.by = "Phase", label = TRUE, reduction = "umap") cat = DimPlot(seurat.obj, group.by = "cc_hclust", label = TRUE, reduction = "umap")
clusters|real_condition|phase|cat
NA
NAsubsetting the cells that fit with hclust and performing clustering on each group
subset(x = seurat.obj, subset = cc_hclust == "CCA")
An object of class Seurat
14410 features across 80 samples within 1 assay
Active assay: RNA (14410 features, 10000 variable features)
3 dimensional reductions calculated: pca, umap, tsneclustering CCI cels
cci_seurat = FindNeighbors(cci_seurat, dims = 1:15)
cci_seurat = FindClusters(cci_seurat, resolution = 1)cl= DimPlot(cci_seurat, group.by = "RNA_snn_res.1",label = TRUE)pap = DimPlot(cci_seurat, group.by = "cat_paper", label = TRUE)cl|pap
identifying CCI cells
cci_markers = FindAllMarkers(cci_seurat, logfc.threshold = 0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')cci_top_markers = cci_markers %>%
group_by(cluster) %>%
slice_min(n = 5, order_by = p_val_adj)VlnPlot(cci_seurat, features = c("Fstl1", "Bgn"))
VlnPlot(cci_seurat, features = c("Tnni3", "Smpx"))
VlnPlot(cci_seurat, features = c("Serpinh1", "Dsp"))
VlnPlot(cci_seurat, features = c("Clca2", "Rbp1"))
VlnPlot(cci_seurat, features = c("Cfh", "B4galt1"))
Fstl1 involved in endothelial cell differentiation and endothelial cell migration and Bgn is a gene that is used for connective tissue metabolism -> lower expression -> cluster 0 = iCM
Tnni3, smpx, dsp used for cardiomycoytes -> cluster 2 = pre-iCM, cluster 1 and 3 are still fibroblasts
cluseter 1 further away from cluster 0 = fibroblastr clusetr 3 = induced fibroblasts
Idents(cci_seurat) = "RNA_snn_res.1"
cci_seurat = RenameIdents(cci_seurat, `0` = "iCM")
cci_seurat = RenameIdents(cci_seurat, `1` = "Fib")
cci_seurat = RenameIdents(cci_seurat, `2` = "piCM")
cci_seurat = RenameIdents(cci_seurat, `3` = "iFib")
clustering CCA cells
cca_seurat = FindClusters(cca_seurat, resolution = 1)
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 80
Number of edges: 2244
Running Louvain algorithm...0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|Maximum modularity in 10 random starts: 0.2948
Number of communities: 3
Elapsed time: 0 secondscl= DimPlot(cca_seurat, group.by = "RNA_snn_res.1",label = TRUE)
pap = DimPlot(cca_seurat, group.by = "cat_paper", label = TRUE)cl|pap
identifying CCA cells
cca_markers = FindAllMarkers(cca_seurat, logfc.threshold = 0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
Calculating cluster 0
Completed [=====>-------------------------------------------------------------------------------------------------] 6% with 0 failures
Completed [======>------------------------------------------------------------------------------------------------] 6% with 0 failures
Completed [======>------------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 31% with 0 failures
Completed [===============================>-----------------------------------------------------------------------] 31% with 0 failures
Completed [===============================>-----------------------------------------------------------------------] 32% with 0 failures
Completed [================================>----------------------------------------------------------------------] 32% with 0 failures
Completed [================================>----------------------------------------------------------------------] 33% with 0 failures
Completed [=================================>---------------------------------------------------------------------] 33% with 0 failures
Completed [==================================>--------------------------------------------------------------------] 34% with 0 failures
Completed [===================================>-------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 65% with 0 failures
Completed [==================================================================>------------------------------------] 65% with 0 failures
Completed [===================================================================>-----------------------------------] 66% with 0 failures
Completed [====================================================================>----------------------------------] 67% with 0 failures
Completed [=====================================================================>---------------------------------] 67% with 0 failures
Completed [=====================================================================>---------------------------------] 68% with 0 failures
Completed [======================================================================>--------------------------------] 68% with 0 failures
Completed [======================================================================>--------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 86% with 0 failures
Completed [========================================================================================>--------------] 86% with 0 failures
Completed [========================================================================================>--------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 88% with 0 failures
Completed [==========================================================================================>------------] 88% with 0 failures
Completed [==========================================================================================>------------] 89% with 0 failures
Completed [===========================================================================================>-----------] 89% with 0 failures
Completed [===========================================================================================>-----------] 90% with 0 failures
Completed [============================================================================================>----------] 90% with 0 failures
Completed [============================================================================================>----------] 91% with 0 failures
Completed [=============================================================================================>---------] 91% with 0 failures
Completed [=============================================================================================>---------] 92% with 0 failures
Completed [==============================================================================================>--------] 92% with 0 failures
Completed [==============================================================================================>--------] 93% with 0 failures
Completed [===============================================================================================>-------] 93% with 0 failures
Completed [===============================================================================================>-------] 94% with 0 failures
Completed [================================================================================================>------] 94% with 0 failures
Completed [================================================================================================>------] 95% with 0 failures
Completed [=================================================================================================>-----] 95% with 0 failures
Completed [=================================================================================================>-----] 96% with 0 failures
Completed [==================================================================================================>----] 96% with 0 failures
Completed [==================================================================================================>----] 97% with 0 failures
Completed [===================================================================================================>---] 97% with 0 failures
Completed [===================================================================================================>---] 98% with 0 failures
Completed [====================================================================================================>--] 98% with 0 failures
Completed [====================================================================================================>--] 99% with 0 failures
Completed [=====================================================================================================>-] 99% with 0 failures
Completed [======================================================================================================>] 100% with 0 failures
Completed [=======================================================================================================] 100% with 0 failures
Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
Completed [==>----------------------------------------------------------------------------------------------------] 3% with 0 failures
Completed [===>---------------------------------------------------------------------------------------------------] 3% with 0 failures
Completed [===>---------------------------------------------------------------------------------------------------] 4% with 0 failures
Completed [====>--------------------------------------------------------------------------------------------------] 4% with 0 failures
Completed [====>--------------------------------------------------------------------------------------------------] 5% with 0 failures
Completed [=====>-------------------------------------------------------------------------------------------------] 5% with 0 failures
Completed [=====>-------------------------------------------------------------------------------------------------] 6% with 0 failures
Completed [======>------------------------------------------------------------------------------------------------] 6% with 0 failures
Completed [======>------------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 31% with 0 failures
Completed [===============================>-----------------------------------------------------------------------] 31% with 0 failures
Completed [===============================>-----------------------------------------------------------------------] 32% with 0 failures
Completed [================================>----------------------------------------------------------------------] 32% with 0 failures
Completed [================================>----------------------------------------------------------------------] 33% with 0 failures
Completed [=================================>---------------------------------------------------------------------] 33% with 0 failures
Completed [==================================>--------------------------------------------------------------------] 34% with 0 failures
Completed [===================================>-------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 65% with 0 failures
Completed [==================================================================>------------------------------------] 65% with 0 failures
Completed [===================================================================>-----------------------------------] 66% with 0 failures
Completed [====================================================================>----------------------------------] 67% with 0 failures
Completed [=====================================================================>---------------------------------] 67% with 0 failures
Completed [=====================================================================>---------------------------------] 68% with 0 failures
Completed [======================================================================>--------------------------------] 68% with 0 failures
Completed [======================================================================>--------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 86% with 0 failures
Completed [========================================================================================>--------------] 86% with 0 failures
Completed [========================================================================================>--------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 88% with 0 failures
Completed [==========================================================================================>------------] 88% with 0 failures
Completed [==========================================================================================>------------] 89% with 0 failures
Completed [===========================================================================================>-----------] 89% with 0 failures
Completed [===========================================================================================>-----------] 90% with 0 failures
Completed [============================================================================================>----------] 90% with 0 failures
Completed [============================================================================================>----------] 91% with 0 failures
Completed [=============================================================================================>---------] 91% with 0 failures
Completed [=============================================================================================>---------] 92% with 0 failures
Completed [==============================================================================================>--------] 92% with 0 failures
Completed [==============================================================================================>--------] 93% with 0 failures
Completed [===============================================================================================>-------] 93% with 0 failures
Completed [===============================================================================================>-------] 94% with 0 failures
Completed [================================================================================================>------] 94% with 0 failures
Completed [================================================================================================>------] 95% with 0 failures
Completed [=================================================================================================>-----] 95% with 0 failures
Completed [=================================================================================================>-----] 96% with 0 failures
Completed [==================================================================================================>----] 96% with 0 failures
Completed [==================================================================================================>----] 97% with 0 failures
Completed [===================================================================================================>---] 97% with 0 failures
Completed [===================================================================================================>---] 98% with 0 failures
Completed [====================================================================================================>--] 98% with 0 failures
Completed [====================================================================================================>--] 99% with 0 failures
Completed [=====================================================================================================>-] 99% with 0 failures
Completed [======================================================================================================>] 100% with 0 failures
Completed [=======================================================================================================] 100% with 0 failures
Done!
Calculating cluster 1
Completed [======>------------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 31% with 0 failures
Completed [===============================>-----------------------------------------------------------------------] 31% with 0 failures
Completed [================================>----------------------------------------------------------------------] 32% with 0 failures
Completed [=================================>---------------------------------------------------------------------] 33% with 0 failures
Completed [==================================>--------------------------------------------------------------------] 34% with 0 failures
Completed [===================================>-------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 65% with 0 failures
Completed [==================================================================>------------------------------------] 65% with 0 failures
Completed [===================================================================>-----------------------------------] 66% with 0 failures
Completed [====================================================================>----------------------------------] 67% with 0 failures
Completed [=====================================================================>---------------------------------] 68% with 0 failures
Completed [======================================================================>--------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 86% with 0 failures
Completed [========================================================================================>--------------] 86% with 0 failures
Completed [========================================================================================>--------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 88% with 0 failures
Completed [==========================================================================================>------------] 88% with 0 failures
Completed [==========================================================================================>------------] 89% with 0 failures
Completed [===========================================================================================>-----------] 89% with 0 failures
Completed [===========================================================================================>-----------] 90% with 0 failures
Completed [============================================================================================>----------] 90% with 0 failures
Completed [============================================================================================>----------] 91% with 0 failures
Completed [=============================================================================================>---------] 91% with 0 failures
Completed [=============================================================================================>---------] 92% with 0 failures
Completed [==============================================================================================>--------] 92% with 0 failures
Completed [==============================================================================================>--------] 93% with 0 failures
Completed [===============================================================================================>-------] 93% with 0 failures
Completed [===============================================================================================>-------] 94% with 0 failures
Completed [================================================================================================>------] 94% with 0 failures
Completed [================================================================================================>------] 95% with 0 failures
Completed [=================================================================================================>-----] 95% with 0 failures
Completed [=================================================================================================>-----] 96% with 0 failures
Completed [==================================================================================================>----] 96% with 0 failures
Completed [==================================================================================================>----] 97% with 0 failures
Completed [===================================================================================================>---] 97% with 0 failures
Completed [===================================================================================================>---] 98% with 0 failures
Completed [====================================================================================================>--] 98% with 0 failures
Completed [====================================================================================================>--] 99% with 0 failures
Completed [=====================================================================================================>-] 99% with 0 failures
Completed [=====================================================================================================>-] 100% with 0 failures
Completed [======================================================================================================>] 100% with 0 failures
Completed [=======================================================================================================] 100% with 0 failures
Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
Completed [======>------------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 31% with 0 failures
Completed [===============================>-----------------------------------------------------------------------] 31% with 0 failures
Completed [================================>----------------------------------------------------------------------] 32% with 0 failures
Completed [=================================>---------------------------------------------------------------------] 33% with 0 failures
Completed [==================================>--------------------------------------------------------------------] 34% with 0 failures
Completed [===================================>-------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 65% with 0 failures
Completed [==================================================================>------------------------------------] 65% with 0 failures
Completed [===================================================================>-----------------------------------] 66% with 0 failures
Completed [====================================================================>----------------------------------] 67% with 0 failures
Completed [=====================================================================>---------------------------------] 68% with 0 failures
Completed [======================================================================>--------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 86% with 0 failures
Completed [========================================================================================>--------------] 86% with 0 failures
Completed [========================================================================================>--------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 88% with 0 failures
Completed [==========================================================================================>------------] 88% with 0 failures
Completed [==========================================================================================>------------] 89% with 0 failures
Completed [===========================================================================================>-----------] 89% with 0 failures
Completed [===========================================================================================>-----------] 90% with 0 failures
Completed [============================================================================================>----------] 90% with 0 failures
Completed [============================================================================================>----------] 91% with 0 failures
Completed [=============================================================================================>---------] 91% with 0 failures
Completed [=============================================================================================>---------] 92% with 0 failures
Completed [==============================================================================================>--------] 92% with 0 failures
Completed [==============================================================================================>--------] 93% with 0 failures
Completed [===============================================================================================>-------] 93% with 0 failures
Completed [===============================================================================================>-------] 94% with 0 failures
Completed [================================================================================================>------] 94% with 0 failures
Completed [================================================================================================>------] 95% with 0 failures
Completed [=================================================================================================>-----] 95% with 0 failures
Completed [=================================================================================================>-----] 96% with 0 failures
Completed [==================================================================================================>----] 96% with 0 failures
Completed [==================================================================================================>----] 97% with 0 failures
Completed [===================================================================================================>---] 97% with 0 failures
Completed [===================================================================================================>---] 98% with 0 failures
Completed [====================================================================================================>--] 98% with 0 failures
Completed [====================================================================================================>--] 99% with 0 failures
Completed [=====================================================================================================>-] 99% with 0 failures
Completed [=====================================================================================================>-] 100% with 0 failures
Completed [======================================================================================================>] 100% with 0 failures
Completed [=======================================================================================================] 100% with 0 failures
Done!
Calculating cluster 2
Completed [=>-----------------------------------------------------------------------------------------------------] 2% with 0 failures
Completed [==>----------------------------------------------------------------------------------------------------] 2% with 0 failures
Completed [==>----------------------------------------------------------------------------------------------------] 3% with 0 failures
Completed [===>---------------------------------------------------------------------------------------------------] 3% with 0 failures
Completed [===>---------------------------------------------------------------------------------------------------] 4% with 0 failures
Completed [====>--------------------------------------------------------------------------------------------------] 4% with 0 failures
Completed [====>--------------------------------------------------------------------------------------------------] 5% with 0 failures
Completed [=====>-------------------------------------------------------------------------------------------------] 5% with 0 failures
Completed [=====>-------------------------------------------------------------------------------------------------] 6% with 0 failures
Completed [======>------------------------------------------------------------------------------------------------] 6% with 0 failures
Completed [======>------------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 31% with 0 failures
Completed [===============================>-----------------------------------------------------------------------] 31% with 0 failures
Completed [===============================>-----------------------------------------------------------------------] 32% with 0 failures
Completed [================================>----------------------------------------------------------------------] 32% with 0 failures
Completed [=================================>---------------------------------------------------------------------] 33% with 0 failures
Completed [==================================>--------------------------------------------------------------------] 34% with 0 failures
Completed [===================================>-------------------------------------------------------------------] 34% with 0 failures
Completed [===================================>-------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 65% with 0 failures
Completed [==================================================================>------------------------------------] 65% with 0 failures
Completed [==================================================================>------------------------------------] 66% with 0 failures
Completed [===================================================================>-----------------------------------] 66% with 0 failures
Completed [====================================================================>----------------------------------] 67% with 0 failures
Completed [=====================================================================>---------------------------------] 68% with 0 failures
Completed [======================================================================>--------------------------------] 68% with 0 failures
Completed [======================================================================>--------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 86% with 0 failures
Completed [========================================================================================>--------------] 86% with 0 failures
Completed [========================================================================================>--------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 88% with 0 failures
Completed [==========================================================================================>------------] 88% with 0 failures
Completed [==========================================================================================>------------] 89% with 0 failures
Completed [===========================================================================================>-----------] 89% with 0 failures
Completed [===========================================================================================>-----------] 90% with 0 failures
Completed [============================================================================================>----------] 90% with 0 failures
Completed [============================================================================================>----------] 91% with 0 failures
Completed [=============================================================================================>---------] 91% with 0 failures
Completed [=============================================================================================>---------] 92% with 0 failures
Completed [==============================================================================================>--------] 92% with 0 failures
Completed [==============================================================================================>--------] 93% with 0 failures
Completed [===============================================================================================>-------] 93% with 0 failures
Completed [===============================================================================================>-------] 94% with 0 failures
Completed [================================================================================================>------] 94% with 0 failures
Completed [================================================================================================>------] 95% with 0 failures
Completed [=================================================================================================>-----] 95% with 0 failures
Completed [=================================================================================================>-----] 96% with 0 failures
Completed [==================================================================================================>----] 96% with 0 failures
Completed [==================================================================================================>----] 97% with 0 failures
Completed [===================================================================================================>---] 97% with 0 failures
Completed [===================================================================================================>---] 98% with 0 failures
Completed [====================================================================================================>--] 98% with 0 failures
Completed [====================================================================================================>--] 99% with 0 failures
Completed [=====================================================================================================>-] 99% with 0 failures
Completed [======================================================================================================>] 100% with 0 failures
Completed [=======================================================================================================] 100% with 0 failures
Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
Completed [====>--------------------------------------------------------------------------------------------------] 5% with 0 failures
Completed [=====>-------------------------------------------------------------------------------------------------] 5% with 0 failures
Completed [=====>-------------------------------------------------------------------------------------------------] 6% with 0 failures
Completed [======>------------------------------------------------------------------------------------------------] 6% with 0 failures
Completed [======>------------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 7% with 0 failures
Completed [=======>-----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 8% with 0 failures
Completed [========>----------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 9% with 0 failures
Completed [=========>---------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 10% with 0 failures
Completed [==========>--------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 11% with 0 failures
Completed [===========>-------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 12% with 0 failures
Completed [============>------------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 13% with 0 failures
Completed [=============>-----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 14% with 0 failures
Completed [==============>----------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 15% with 0 failures
Completed [===============>---------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 16% with 0 failures
Completed [================>--------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 17% with 0 failures
Completed [=================>-------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 18% with 0 failures
Completed [==================>------------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 19% with 0 failures
Completed [===================>-----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 20% with 0 failures
Completed [====================>----------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 21% with 0 failures
Completed [=====================>---------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 22% with 0 failures
Completed [======================>--------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 23% with 0 failures
Completed [=======================>-------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 24% with 0 failures
Completed [========================>------------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 25% with 0 failures
Completed [=========================>-----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 26% with 0 failures
Completed [==========================>----------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 27% with 0 failures
Completed [===========================>---------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 28% with 0 failures
Completed [============================>--------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 29% with 0 failures
Completed [=============================>-------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 30% with 0 failures
Completed [==============================>------------------------------------------------------------------------] 31% with 0 failures
Completed [===============================>-----------------------------------------------------------------------] 31% with 0 failures
Completed [===============================>-----------------------------------------------------------------------] 32% with 0 failures
Completed [================================>----------------------------------------------------------------------] 32% with 0 failures
Completed [=================================>---------------------------------------------------------------------] 33% with 0 failures
Completed [==================================>--------------------------------------------------------------------] 34% with 0 failures
Completed [===================================>-------------------------------------------------------------------] 34% with 0 failures
Completed [===================================>-------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 35% with 0 failures
Completed [====================================>------------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 36% with 0 failures
Completed [=====================================>-----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 37% with 0 failures
Completed [======================================>----------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 38% with 0 failures
Completed [=======================================>---------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 39% with 0 failures
Completed [========================================>--------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 40% with 0 failures
Completed [=========================================>-------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 41% with 0 failures
Completed [==========================================>------------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 42% with 0 failures
Completed [===========================================>-----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 43% with 0 failures
Completed [============================================>----------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 44% with 0 failures
Completed [=============================================>---------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 45% with 0 failures
Completed [==============================================>--------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 46% with 0 failures
Completed [===============================================>-------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 47% with 0 failures
Completed [================================================>------------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 48% with 0 failures
Completed [=================================================>-----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 49% with 0 failures
Completed [==================================================>----------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 50% with 0 failures
Completed [===================================================>---------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 51% with 0 failures
Completed [====================================================>--------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 52% with 0 failures
Completed [=====================================================>-------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 53% with 0 failures
Completed [======================================================>------------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 54% with 0 failures
Completed [=======================================================>-----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 55% with 0 failures
Completed [========================================================>----------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 56% with 0 failures
Completed [=========================================================>---------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 57% with 0 failures
Completed [==========================================================>--------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 58% with 0 failures
Completed [===========================================================>-------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 59% with 0 failures
Completed [============================================================>------------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 60% with 0 failures
Completed [=============================================================>-----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 61% with 0 failures
Completed [==============================================================>----------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 62% with 0 failures
Completed [===============================================================>---------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 63% with 0 failures
Completed [================================================================>--------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 64% with 0 failures
Completed [=================================================================>-------------------------------------] 65% with 0 failures
Completed [==================================================================>------------------------------------] 65% with 0 failures
Completed [==================================================================>------------------------------------] 66% with 0 failures
Completed [===================================================================>-----------------------------------] 66% with 0 failures
Completed [====================================================================>----------------------------------] 67% with 0 failures
Completed [=====================================================================>---------------------------------] 68% with 0 failures
Completed [======================================================================>--------------------------------] 68% with 0 failures
Completed [======================================================================>--------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 69% with 0 failures
Completed [=======================================================================>-------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 70% with 0 failures
Completed [========================================================================>------------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 71% with 0 failures
Completed [=========================================================================>-----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 72% with 0 failures
Completed [==========================================================================>----------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 73% with 0 failures
Completed [===========================================================================>---------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 74% with 0 failures
Completed [============================================================================>--------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 75% with 0 failures
Completed [=============================================================================>-------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 76% with 0 failures
Completed [==============================================================================>------------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 77% with 0 failures
Completed [===============================================================================>-----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 78% with 0 failures
Completed [================================================================================>----------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 79% with 0 failures
Completed [=================================================================================>---------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 80% with 0 failures
Completed [==================================================================================>--------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 81% with 0 failures
Completed [===================================================================================>-------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 82% with 0 failures
Completed [====================================================================================>------------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 83% with 0 failures
Completed [=====================================================================================>-----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 84% with 0 failures
Completed [======================================================================================>----------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 85% with 0 failures
Completed [=======================================================================================>---------------] 86% with 0 failures
Completed [========================================================================================>--------------] 86% with 0 failures
Completed [========================================================================================>--------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 87% with 0 failures
Completed [=========================================================================================>-------------] 88% with 0 failures
Completed [==========================================================================================>------------] 88% with 0 failures
Completed [==========================================================================================>------------] 89% with 0 failures
Completed [===========================================================================================>-----------] 89% with 0 failures
Completed [===========================================================================================>-----------] 90% with 0 failures
Completed [============================================================================================>----------] 90% with 0 failures
Completed [============================================================================================>----------] 91% with 0 failures
Completed [=============================================================================================>---------] 91% with 0 failures
Completed [=============================================================================================>---------] 92% with 0 failures
Completed [==============================================================================================>--------] 92% with 0 failures
Completed [==============================================================================================>--------] 93% with 0 failures
Completed [===============================================================================================>-------] 93% with 0 failures
Completed [===============================================================================================>-------] 94% with 0 failures
Completed [================================================================================================>------] 94% with 0 failures
Completed [================================================================================================>------] 95% with 0 failures
Completed [=================================================================================================>-----] 95% with 0 failures
Completed [=================================================================================================>-----] 96% with 0 failures
Completed [==================================================================================================>----] 96% with 0 failures
Completed [==================================================================================================>----] 97% with 0 failures
Completed [===================================================================================================>---] 97% with 0 failures
Completed [===================================================================================================>---] 98% with 0 failures
Completed [====================================================================================================>--] 98% with 0 failures
Completed [====================================================================================================>--] 99% with 0 failures
Completed [=====================================================================================================>-] 99% with 0 failures
Completed [======================================================================================================>] 100% with 0 failures
Completed [=======================================================================================================] 100% with 0 failures
Done!cca_top_markers = cca_markers %>%
group_by(cluster) %>%
slice_min(n = 5, order_by = p_val_adj)VlnPlot(cca_seurat, features = c("Dab2", "Kcnab1"))
VlnPlot(cca_seurat, features = c("Cenpf", "Pttg1"))
VlnPlot(cca_seurat, features = c("Upk1b", "Timp3"))
NA
NAdab2 involved in endothelial stuf -> 0 is probably induced cardiomyocyet Upk1b is involved in epithelial stuff -> 2 is porbably fibroblasts 1 - induced fibroblasts
Idents(cca_seurat) = "RNA_snn_res.1"
cca_seurat = RenameIdents(cca_seurat, `0` = "iCM")
cca_seurat = RenameIdents(cca_seurat, `1` = "iFib")
cca_seurat = RenameIdents(cca_seurat, `2` = "Fib")
DimPlot(cca_seurat, label = TRUE)
SC Transform
seurat.sc = CreateSeuratObject(counts = exp)
seurat.sc = SCTransform(seurat.sc)seurat.sc = RunPCA(seurat.sc, features = VariableFeatures(seurat.sc))identified_cells = identified_cells[match(rownames(seurat.sc@meta.data), rownames(identified_cells)),]
seurat.sc@meta.data$cc_paper = identified_cells$CC
seurat.sc@meta.data$cat_paper = identified_cells$stage
seurat.sc = RunUMAP(seurat.sc, dims = 1:15)
seurat.sc = FindNeighbors(seurat.sc, dims = 1:15)
seurat.sc = FindClusters(seurat.sc, resolution = 1.75)seurat.sc = CellCycleScoring(seurat.sc, s.features = s.genes, g2m.features = g2m.genes)clusters = DimPlot(seurat.sc, group.by = "SCT_snn_res.1.75", label = TRUE, reduction = "umap")
real_condition = DimPlot(seurat.sc, group.by = "cc_paper", label = TRUE, reduction = "umap")
phase = DimPlot(seurat.sc, group.by = "Phase", label = TRUE, reduction = "umap")
cat = DimPlot(seurat.sc, group.by = "cat_paper", label = TRUE, reduction = "umap")
clusters|real_condition|phase|cat
---
title: "R Notebook"
output: html_notebook
---

This is an [R Markdown](http://rmarkdown.rstudio.com) Notebook. When you execute code within the notebook, the results appear beneath the code. 

Try executing this chunk by clicking the *Run* button within the chunk or by placing your cursor inside it and pressing *Cmd+Shift+Enter*. 

```{r}
library("devtools")
install_github("jw156605/SLICER")
library(Seurat)
library(readr)
library(tidyverse)
library(HGC) 
library(latticeExtra)
library(lattice) 
library(RColorBrewer)
library(clusterProfiler)
library(org.Mm.eg.db)
library(AnnotationDbi)
```


```{r}
exp = read_csv("normalized_data.csv")
exp = discard(exp,~all(is.na(.) |.  == ""))
exp = distinct(exp, `...1`, .keep_all = TRUE)
# filtering out the reprogramming transcription factors 
exp = filter(exp, !`...1`%in% c("Mef2c", "Gata4", "Tbx5"))
exp = column_to_rownames(exp, var="...1")

```
```{r}

seurat.obj = CreateSeuratObject(counts = exp)
```
```{r}
seurat.obj = NormalizeData(seurat.obj)
seurat.obj = FindVariableFeatures(seurat.obj, selection.method =  "vst", nfeatures = 10000)
all.genes = rownames(seurat.obj)
seurat.obj = ScaleData(seurat.obj, features = all.genes)
seurat.obj = RunPCA(seurat.obj, features =  VariableFeatures(seurat.obj))

```
```{r}
ElbowPlot(seurat.obj)
```

```{r}
seurat.obj = FindNeighbors(seurat.obj, dims = 1:15)
```

```{r}
seurat.obj = FindClusters(seurat.obj, resolution = 1.75)
```
```{r}
identified_cells = read.csv("paper_cell_states.csv", row.names = 1, header=TRUE)
```
```{r}
identified_cells = identified_cells[match(rownames(seurat.obj@meta.data), rownames(identified_cells)),]
seurat.obj@meta.data$cc_paper = identified_cells$CC
seurat.obj@meta.data$cat_paper = identified_cells$stage
seurat.obj@meta.data$cc_hclust = "CCI"
seurat.obj@meta.data[active_cells,]$cc_hclust = "CCA"

```


```{r}
Idents(seurat.obj)  = "RNA_snn_res.1.75"
```

```{r}
seurat.obj = RunUMAP(seurat.obj, dims = 1:15)
```
```{r}
seurat.obj = RunTSNE(seurat.obj, dims = 1:15)
DimPlot(seurat.obj, reduction = "tsne", group.by = 'RNA_snn_res.1.75')
``` 

```{r}
markers = FindAllMarkers(seurat.obj, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
```
```{r}
top_markers = markers %>%
    group_by(cluster) %>%
    slice_max(n = 2, order_by = avg_log2FC)
```

```{r}
FeaturePlot(seurat.obj, features = c("Dhrs3"), min.cutoff = 'q10')
```
```{r}
VlnPlot(seurat.obj, features = c("Rbp1", "Dhrs3"))
VlnPlot(seurat.obj, features = c("Fstl1", "Bgn"))
VlnPlot(seurat.obj, features = c("Serpinh1", "Dsp"))
VlnPlot(seurat.obj, features = c("Prc1", "Birc5"))
```
```{r}
## cell cycle 
s.genes <- str_to_title(cc.genes$s.genes)
g2m.genes <- str_to_title(cc.genes$g2m.genes)

seurat.obj = CellCycleScoring(seurat.obj, s.features = s.genes, g2m.features = g2m.genes)
```


```{r}
clusters = DimPlot(seurat.obj, group.by = "RNA_snn_res.1.75", label = TRUE, reduction = "umap")
real_condition = DimPlot(seurat.obj, group.by = "cc_paper", label = TRUE, reduction = "umap") 
phase = DimPlot(seurat.obj, group.by = "Phase", label = TRUE, reduction = "umap") 
cat = DimPlot(seurat.obj, group.by = "cc_hclust", label = TRUE, reduction = "umap") 

clusters|real_condition|phase|cat


```

## subsetting the cells that fit with hclust and performing clustering on each group 

```{r}
cca_seurat = subset(x = seurat.obj, subset = cc_hclust == "CCA")
cci_seurat = subset(x = seurat.obj, subset = cc_hclust == "CCI")

```

## clustering CCI cels 

```{r}
cci_seurat = FindNeighbors(cci_seurat, dims = 1:15)
cci_seurat = FindClusters(cci_seurat, resolution = 1)
```

```{r}
cl= DimPlot(cci_seurat, group.by = "RNA_snn_res.1",label = TRUE)
pap = DimPlot(cci_seurat, group.by = "cat_paper", label = TRUE)
cl|pap
```
## identifying CCI cells 

```{r}
cci_markers = FindAllMarkers(cci_seurat, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
```
```{r}
cci_top_markers = cci_markers %>%
    group_by(cluster) %>%
    slice_min(n = 5, order_by = p_val_adj)
```

```{r}
VlnPlot(cci_seurat, features = c("Fstl1", "Bgn"))
VlnPlot(cci_seurat, features = c("Tnni3", "Smpx"))
VlnPlot(cci_seurat, features = c("Serpinh1", "Dsp"))
VlnPlot(cci_seurat, features = c("Clca2", "Rbp1"))
VlnPlot(cci_seurat, features = c("Cfh", "B4galt1"))

```
#### 

Fstl1 involved in endothelial cell differentiation and endothelial cell migration and Bgn is a gene that is used for connective tissue metabolism -> lower expression -> cluster 0 = iCM 

Tnni3, smpx, dsp used for cardiomycoytes -> cluster 2 = pre-iCM, cluster 1 and 3 are still fibroblasts 

cluseter 1 further away from cluster 0 = fibroblastr
clusetr 3 = induced fibroblasts

```{r}
Idents(cci_seurat)  = "RNA_snn_res.1"
cci_seurat = RenameIdents(cci_seurat, `0` = "iCM")
cci_seurat = RenameIdents(cci_seurat, `1` = "Fib")
cci_seurat = RenameIdents(cci_seurat, `2` = "piCM")
cci_seurat = RenameIdents(cci_seurat, `3` = "iFib")

```

```{r}
DimPlot(cci_seurat, label = TRUE)

```
## clustering CCA cells


```{r}
cca_seurat = FindNeighbors(cca_seurat, dims = 1:15)
cca_seurat = FindClusters(cca_seurat, resolution = 1)
```

```{r}
cl= DimPlot(cca_seurat, group.by = "RNA_snn_res.1",label = TRUE)
pap = DimPlot(cca_seurat, group.by = "cat_paper", label = TRUE)
cl|pap
```
## identifying CCA cells 

```{r}
cca_markers = FindAllMarkers(cca_seurat, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
```
```{r}
cca_top_markers = cca_markers %>%
    group_by(cluster) %>%
    slice_min(n = 5, order_by = p_val_adj)
```

```{r}
VlnPlot(cca_seurat, features = c("Dab2", "Kcnab1"))
VlnPlot(cca_seurat, features = c("Cenpf", "Pttg1"))
VlnPlot(cca_seurat, features = c("Upk1b", "Timp3"))


```
#### 

dab2 involved in endothelial stuf -> 0 is probably induced cardiomyocyet
Upk1b is involved in epithelial stuff -> 2 is porbably fibroblasts 
1 - induced fibroblasts

```{r}
Idents(cca_seurat)  = "RNA_snn_res.1"
cca_seurat = RenameIdents(cca_seurat, `0` = "iCM")
cca_seurat = RenameIdents(cca_seurat, `1` = "iFib")
cca_seurat = RenameIdents(cca_seurat, `2` = "Fib")


```

```{r}
DimPlot(cca_seurat, label = TRUE)

```

## SC Transform       
```{r}
seurat.sc = CreateSeuratObject(counts = exp)
seurat.sc = SCTransform(seurat.sc)
```
```{r}
seurat.sc = RunPCA(seurat.sc, features =  VariableFeatures(seurat.sc))
```

```{r}
identified_cells = identified_cells[match(rownames(seurat.sc@meta.data), rownames(identified_cells)),]
seurat.sc@meta.data$cc_paper = identified_cells$CC
seurat.sc@meta.data$cat_paper = identified_cells$stage

seurat.sc = RunUMAP(seurat.sc, dims = 1:15)
seurat.sc = FindNeighbors(seurat.sc, dims = 1:15)
seurat.sc = FindClusters(seurat.sc, resolution = 1.75)
```

```{r}
seurat.sc = CellCycleScoring(seurat.sc, s.features = s.genes, g2m.features = g2m.genes)
```

```{r}
clusters = DimPlot(seurat.sc, group.by = "SCT_snn_res.1.75", label = TRUE, reduction = "umap")
real_condition = DimPlot(seurat.sc, group.by = "cc_paper", label = TRUE, reduction = "umap") 
phase = DimPlot(seurat.sc, group.by = "Phase", label = TRUE, reduction = "umap") 
cat = DimPlot(seurat.sc, group.by = "cat_paper", label = TRUE, reduction = "umap") 

clusters|real_condition|phase|cat

```

